Hi , I have been trying to use limma to construct linear model of my normalized affymetrix data, but the program gives me an error at the last step of the calculation by empirical bayes. Can someone using the package give a comment on my error. > design <- model.matrix(~ -1+factor(c(1,2,3,4,5,1,2,3,4,5))) > colnames(design) <- c("group1", "group2", "group3", "group4", "group5") > fit <- lmFit(esetsarco, design) > contrast.matrix <- makeContrasts(group1-group2, group1-group3, group1-group4, group1-group5, group2-group3, group2-group4, group2-group5, group3-group4, group3-group5, levels=design) > fit2 <- contrasts.fit(fit, contrast.matrix) > fit2 <- eBayes(fit2) Error in ebayes(fit = fit, proportion = proportion, std.coef = std.coef) : No residual degrees of freedom in linear model fits Thanks Amin Momin

There was a bug in limma that kept it from using an exprSet correctly. The development version contains the fixed version of lmFit. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Amin Momin" <gtg269c@mail.gatech.edu> 11/21/03 10:00AM >>> Hi , I have been trying to use limma to construct linear model of my normalized affymetrix data, but the program gives me an error at the last step of the calculation by empirical bayes. Can someone using the package give a comment on my error. > design <- model.matrix(~ -1+factor(c(1,2,3,4,5,1,2,3,4,5))) > colnames(design) <- c("group1", "group2", "group3", "group4", "group5") > fit <- lmFit(esetsarco, design) > contrast.matrix <- makeContrasts(group1-group2, group1-group3, group1-group4, group1-group5, group2-group3, group2-group4, group2-group5, group3-group4, group3-group5, levels=design) > fit2 <- contrasts.fit(fit, contrast.matrix) > fit2 <- eBayes(fit2) Error in ebayes(fit = fit, proportion = proportion, std.coef = std.coef) : No residual degrees of freedom in linear model fits Thanks Amin Momin _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor